tbuckley/cabot-search huggingface dataset:
Abstract LB024: Cancer stem cells are enriched in human recurrent glioblastoma
Authors: Xuanhua Peter Xie, Mungunsarnai Ganbold, Alicia Pedraza, Luis Parada
Journal: Cancer Research (2022)

Abstract A number of studies have described an essential role of cancer stem cells (CSC) in glioblastoma (GBM) progression and recurrence based on isolation by candidate markers. However, a systematic evaluation of the proposed CSC in paired human primary and recurrent glioblastoma has been lacking and whether they represent a unified cell type with conserved features over tumor evolution is unresolved. In this study, we used human patient derived xenografts (PDX) to investigate the status of these cells in patients following therapeutics and recurrence. Firstly, to ensure the fidelity of tumor heterogeneity in serially passaged orthotopic GBM PDX, we collected samples at different passages and performed whole tumor single cell RNA sequencing analysis. The results illustrate the preservation of all unsupervised transcriptional cell clusters through multiple passages. Furthermore, treatment of tumor bearing mice with temozolomide, the standard of care chemotherapeutic drug for glioblastoma patients, increased apoptosis and decreased tumor cell burden but spared CSC. We then turned to paired human primary and recurrent GBM samples to inquire cancer stem cell marker expression and cell distribution. In all three pairs of PDX studied, cancer stem cell marker F3 serves as a reliable means to isolate sphere formation cells and is augmented in the recurrent samples. Inspection of whole tumors with single cell RNA sequencing nails down the enrichment of CSC in recurrent tumors, thus emphasizing the importance to eradicate these cells in future therapeutics. Citation Format: Xuanhua Peter Xie, Mungunsarnai Ganbold, Alicia Pedraza, Luis Parada. Cancer stem cells are enriched in human recurrent glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB024.
Abstract 89: The microRNA-3622b-3p contributes to tumor progression and metastasis through an miR-3622-AIFM2 axis in prostate cancer
Authors: Lizhong Wang, Chao Zhang, Ping Ye
Journal: Cancer Research (2022)

Abstract microRNA (miR)-3622 family is composed of two members, miR-3622a/b, but their roles remain debatable. In the present study, we found that expression of miR-3622a was lower, whereas expression of miR-3622b-3p was higher in human prostate cancer tissues than in normal prostate tissues. miR-3622a-3p inhibited cell migration and invasion of human prostate cancer cells, whereas miR-3622b-3p facilitated cell proliferation, migration, and invasion. To address the opposing roles of miR-3622 family members in various human prostate cancer cell lines, we knocked out endogenous miR-3622, including both miR-3622a/b. Our results showed that miR-3622 knockout reduced cell proliferation, migration, and invasion in vitro and tumor growth and metastasis in vivo. Furthermore, we found that AIFM2, a direct target of miR-3622b-3p, is responsible for miR-3622 knockout-induced apoptosis, identifying an miR-3622-AIFM2 axis that contributes to oncogenic function during tumor progression. The results show that miR-3622b-3p is upregulated in human prostate cancers and has an oncogenic function in tumor progression and metastasis through an miR-3622-AIFM2 axis. Citation Format: Lizhong Wang, Chao Zhang, Ping Ye. The microRNA-3622b-3p contributes to tumor progression and metastasis through an miR-3622-AIFM2 axis in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 89.
Abstract 93: Soluble mesothelin acts as a signaling molecule
Authors: Theressa Ewa, Leela Avula, Sarah Joseph, Michael Rudloff, Samantha Sevilla, Vishal Koparde, Xianyu Zhang, Christine Alewine
Journal: Cancer Research (2022)

Abstract Mesothelin (MSLN) is a cell surface glycoprotein that is expressed by most pancreatic ductal adenocarcinoma (PDAC) and is used as a target for anti-cancer therapy. MSLN expression appears to make pancreatic cancer more aggressive. Previously, we found that MSLN KO PDAC cells grow in culture and as subcutaneous tumors similarly to wild-type (WT) cells but form intraperitoneal metastases poorly. MSLN pre-cursor (pre-MSLN) is a 71-kD glycosylphosphatidylinositol (GPI)-anchored protein that is cleaved intracellularly to make the 31-kD secreted protein Megakaryocyte Potentiating Factor (MPF), and a 40-kD mature MSLN (mMSLN) that retains membrane attachment. The mMSLN can be shed from the cell surface by the action of specific proteases, resulting in release of soluble MSLN (sMSLN) to both the tumor microenvironment and serum. The goal of this study is to see if sMSLN promotes cancer cell aggressiveness. We transduced MSLN KO pancreas cancer cells to express: 1) a mutant, secreted-only pre-MSLN (includes WT MPF) with a C-terminal truncation (MSLNΔ599) that prevents GPI-linkage of MSLN to the membrane, and 2) truncated pre-MSLN consisting of MPF only. Results show that complementation of KO cells with MPF or MSLNΔ599 does not rescue the MSLN KO phenotype, while MSLNΔ599 bearing a Y318A point mutation that disrupts the binding of MSLN to MUC16/CA125 does restore growth of peritoneal metastasis. We performed RNA-deep sequencing on MSLN KO cells exposed to WT or Y318A sMSLN from conditioned medium. We identified 2000 genes that were differentially expressed across the treatment groups. Exposure to sMSLN resulted in changes in expression of cell adhesion and sterol biosynthetic synthesis pathway genes. Individual genes that were top hits were also identified and are under investigation. Exposure to sMSLN changes the transcriptomic program of pancreas cancer cells and may promote peritoneal colonization. Citation Format: Theressa Ewa, Leela Avula, Sarah Joseph, Michael Rudloff, Samantha Sevilla, Vishal Koparde, Xianyu Zhang, Christine Alewine. Soluble mesothelin acts as a signaling molecule [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 93.
Hepatitis B virus-specific CD4 T cell responses differentiate functional cure from chronic surface antigen+ infection
Authors: Ruben C. Hoogeveen, Suzan Dijkstra, Lea M. Bartsch, Hannah K. Drescher, Jasneet Aneja, Maxwell P. Robidoux, James A. Cheney, Joerg Timm, Adam Gehring, Paulo Sergio Fonseca de Sousa, Lya Ximenez, Luis Baiao Peliganga, Anita Pitts, Fiona B. Evans, André Boonstra, Arthur Y. Kim, Lia L. Lewis-Ximenez, Georg M. Lauer
Journal: Journal of Hepatology (2022)
Abstract 5156: Multiplexed EGFR mutation detection with C797S and T790M allelic context using six-color digital PCR
Authors: Wei Yang, Mari Christensen, Jennifer K. Chan, Julie Tsai, Nancy Patten, Ha B. Tran, Grant R. Hillman, Yu Chuan Tai, Patrick Bogard, Claudia M. Litterst, Victoria H. Brophy, Nick Newton, Christopher D. Nelson, Wouter J. Pattje
Journal: Cancer Research (2022)

Abstract Non-small cell lung cancer (NSCLC) patients harboring activating mutations in epidermal growth factor receptor (EGFR) are benefited from Tyrosine Kinase Inhibitor (TKI) targeted therapy. However, more than 50% of patients receiving the first or second generations of TKI develop a resistance mutation, EGFR-T790M, and they will need to switch to the third-generation TKI (Osimertinib). Upon treatment, a second acquired mutation, EGFR-C797S, leads to the resistance to Osimertinib. If the C797S and T790M mutations are located in trans, a combination of the first and third-generation of TKI(s) may offer some benefit to the patient. The impact of the allelic context to the subsequent treatment is yet to be established and thus an assay identifying C797S and T790M allelic context may serve as a useful research tool. In recent years, digital PCR has emerged to be an ultra-sensitive method in non-invasive identification and monitoring of cancer mutations. However, compared to qPCR and NGS methods, current digital PCR assays are limited by the number of biomarkers that can be incorporated in a single assay and the maximum sample volume that can be screened in one test. In this study, we describe a multiplex digital PCR assay for quantitative detection of EGFR sensitizing and resistance mutations, and identification of C797S and T790M allelic context, using a 6-color digital PCR system that allows high sample volume utilization. The sensitivity and specificity of this multiplex dPCR assay were tested using a panel of contrived cell-free DNA samples. Individual mutations can be detected at as low as 0.2% fractional abundance level. Furthermore, we compared the performance of the multiplex with the 2-color droplet digital PCR Expert Design Assays on the Bio-Rad QX200 ddPCR system, using a commercial multiplex cfDNA reference standard set. The multiplexed EGFR mutation assay on the 6-color Digital LightCycler® System is a promising method for rapid and sensitive monitoring of EGFR mutations in cell-free DNA. Citation Format: Wei Yang, Mari Christensen, Jennifer K. Chan, Julie Tsai, Nancy Patten, Ha B. Tran, Grant R. Hillman, Yu Chuan Tai, Patrick Bogard, Claudia M. Litterst, Victoria H. Brophy, Nick Newton, Christopher D. Nelson, Wouter J. Pattje. Multiplexed EGFR mutation detection with C797S and T790M allelic context using six-color digital PCR [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5156.
Abstract 2052: LAMP1 targeting of the large T antigen of Merkel cell polyomavirus elicits potent CD4+ T cell responses, tumor inhibition, and provides rationale for first-in-human trial
Authors: Claire Buchta Rosean, Mohan Karkada, David M. Koelle, Paul Nghiem, Teri Heiland
Journal: Cancer Research (2022)

Abstract The majority of Merkel cell carcinomas (MCC), a rare and highly aggressive type of neuroendocrine skin cancer, are associated with Merkel cell polyomavirus (MCPyV) infection. MCPyV integrates into the host genome, resulting in expression of a truncated form of the viral large T antigen (LT) in infected cells and thus making LT an attractive target for therapeutic cancer vaccines. We designed a cancer vaccine that promotes potent, antigen-specific CD4+ T cell responses to MCPγV-LT. To activate antigen-specific CD4+ T cells in vivo, we utilized our nucleic acid platform, UNITE࣪ (UNiversal Intracellular Targeted Expression), which fuses a tumor-associated antigen with lysosomal-associated membrane protein 1 (LAMP1). This lysosomal targeting technology results in enhanced antigen presentation and a balanced T cell response. LTS220A, encoding a mutated form of MCPγV-LT that diminishes its pro-oncogenic properties, was introduced into the UNITE࣪ platform. In pre-clinical studies, vaccination with LTS220A-UNITE࣪ (ITI-3000) induced antigen-specific CD4+ T cells that were sufficient to delay tumor growth, and this effect was dependent on their ability to produce IFNγ. Moreover, ITI-3000 induced a favorable tumor microenvironment (TME), including significantly enhanced numbers of CD4+ and CD8+ T cells as well as NK and NKT cells. These findings strongly suggest that in pre-clinical studies, DNA vaccination using the UNITE࣪ platform enhances CD4+ T cell responses to MCPγV-LT that result in significant anti-tumor immune responses. We are planning a first-in-human (FIH) Phase 1 open-label study to evaluate the safety, tolerability, and immunogenicity of ITI-3000 in patients with polyomavirus-positive MCC. Patients will receive up to four intramuscular vaccinations of 4mg of ITI-3000 using the PharmaJet Stratis® needle-free injection system. The primary objectives will be safety and tolerability, observing dose-limiting toxicities, serious adverse events, standard clinical assessments, and safety laboratory parameters. Immunogenicity of the vaccine will be measured by peripheral blood assessments of T cell activation using ELISpot and flow cytometry assays. Citation Format: Claire Buchta Rosean, Mohan Karkada, David M. Koelle, Paul Nghiem, Teri Heiland. LAMP1 targeting of the large T antigen of Merkel cell polyomavirus elicits potent CD4+ T cell responses, tumor inhibition, and provides rationale for first-in-human trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2052.
Abstract 3152: IFN-gamma stimulated cryopreserved mesenchymal stromal cells for treatment of radiation induced xerostomia
Authors: Cristina Paz, Grace Blitzer, Annemarie Glassey, Kwangok P. Nickel, Jayeeta Giri, Andrea Pennati, Daniel Robbins, Tadeas Lunga, Susan Thibeault, Jacques Galipeau, Randall Kimple
Journal: Cancer Research (2022)

Abstract Purpose/Objectives: There is a critical need for a treatment that will safely and effectively alleviate radiation-induced xerostomia (RIX). Head and neck radiation results in hyposalivation and altered sialochemistry which patients experience as xerostomia. We performed a preclinical and a pilot clinical study to determine if IFN-ɣ stimulated marrow-derived mesenchymal stromal cells (MSC(M)) from HNC patients could function as a source of autologous cells for the treatment of RIX and as a tool in preclinical murine studies of RIX. Materials/Methods: Bone marrow aspirates from HNC patients previously treated with chemoradiation were obtained (IRB #2019-0497, NCT 04007081). MSC(M)s were isolated from bone marrow. MSC(M) were expanded in culture, surface marker expression was confirmed via flow cytometry, stimulated with IFN-ɣ, and cryopreserved. Thawed MSC(M)s were profiled to evaluate their functionality after cryorecovery. Cells were tested for their ability to stimulate salivary production in a murine model of RIX by injecting 1x106 cells into the submandibular gland (SMG) one week after a single 15 Gy fraction of radiation. Efficacy was evaluated by saliva production and histology. Results: MSC(M)s from six patients were expanded to &amp;gt;20x106 cells (median 15.5, range of 8-20 days). Post-thaw cultures demonstrated robust growth, with a median doubling time of 3.1 days. Cultured cells showed an MSC(M) phenotype, positive for CD73, CD90, and CD105 and negative for CD14, CD20, CD34, or CD45. IFN-ɣ stimulated MSC(M)s had immunomodulatory potential based on increased expression of IDO, ICAM-1, PD-L1, MHC I and MHC II expression compared with non-stimulated MSC(M)s (391%, 263%, 114%, 70% and 196% percent increase respectively). In a murine model of RIX, radiation resulted in structural changes to the gland as evidenced by increased fibrosis, decreased acinar size, and immune cell infiltration. Injection of MSC(M)s to the SMG following radiation resulted in improved saliva production, a reduction in fibrosis, and an increase in the size and density of acini within the tissue compared to control. Conclusions: These data strongly support the feasibility of a first-in-human clinical trial of autologous IFN-ɣ stimulated MSC(M)s to treat RIX and the potential of using human-derived MSC(M)s in future murine studies of RIX. Citation Format: Cristina Paz, Grace Blitzer, Annemarie Glassey, Kwangok P. Nickel, Jayeeta Giri, Andrea Pennati, Daniel Robbins, Tadeas Lunga, Susan Thibeault, Jacques Galipeau, Randall Kimple. IFN-gamma stimulated cryopreserved mesenchymal stromal cells for treatment of radiation induced xerostomia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3152.
Abstract 2194: Rapid interrogation of colon cancer driver genes in vivo using split Cre and CRISPR-Cas9
Authors: Daniel Zhang, Peter Westcott, Santiago Naranjo, Haley Hauck, William Rideout, Nate Sacks, Arjun Bhutkar, Justin Patten, Norihiro Goto, Joseph Sedlak, Tyler Jacks
Journal: Cancer Research (2022)

Abstract Colorectal cancer (CRC) is the second leading cause of cancer-related deaths worldwide, with a five-year survival rate of only 63% with current treatment regimens. While genetically engineered mouse models (GEMMs) have contributed widely to our understanding of the underlying genetics and molecular mechanisms of the disease, major limitations exist. Most models of CRC lack flexibility to initiate focal adenocarcinomas with different genetic perturbations within the native microenvironment of the distal colon. Specifically, no autochthonous model of metastatic CRC compatible with in vivo CRISPR-Cas9 genome engineering has been described. Therefore, we developed a novel split Cre-recombinase system restricting activation of oncogenic KrasG12D and deletion of the tumor suppressor gene (TSG) Trp53 to Lgr5+ stem cells of the colon crypts. Importantly, these events are not only critical drivers of CRC progression and metastasis in mice and humans but can also lead to non-specific transformation of the surrounding colonic stroma. By expressing one half of Cre from the endogenous Lgr5 locus and other half via colonoscopy-guided submucosal injection of lentivirus, we restricted Cre-mediated recombination to enterocytes. Lentivirus was also engineered to express a single guide RNA (sgRNA) against Apc, facilitating tumor initiation via deletion of this critical CRC TSG in mice expressing Cas9. A second sgRNA was included to facilitate rapid interrogation of putative cancer driver genes. As proof-of-principle, we targeted Smad4, a critical suppressor of metastasis in CRC, and observed adenocarcinoma formation and liver metastases with complete recombination and editing of all targeted genes. To prioritize candidate TSGs for future in vivo interrogation, we applied MutSigCV to large human sequencing datasets and identified genes significantly co-mutated with APC and KRAS in CRC. Altogether, this faithful and tractable model of CRC can be used for rapid functional interrogation of TSGs and should accelerate downstream mechanistic and preclinical studies. Citation Format: Daniel Zhang, Peter Westcott, Santiago Naranjo, Haley Hauck, William Rideout, Nate Sacks, Arjun Bhutkar, Justin Patten, Norihiro Goto, Joseph Sedlak, Tyler Jacks. Rapid interrogation of colon cancer driver genes in vivo using split Cre and CRISPR-Cas9 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2194.
Abstract 5009: DKK1 is a potential target for enhancing the efficiency of radioimmunotherapy in head and neck squamous carcinoma
Authors: Xinyu YE, JIAN Zhang, Yi Lu, Yingxuan Gong, Xinyu Jiang, Yueming Li, Yinghao Wang, Xiuzhi Li, Jingwen Liu, Rencui Quan
Journal: Cancer Research (2022)

Abstract Immune checkpoint inhibitors (ICIs) have been approved to treat various types of tumors, including head and neck squamous carcinoma (HNSC). However, most HNSC patients do not respond to ICIs. Radioimmunotherapy has been proposed to enhance the immune response rate in HNSC. Herein, we aimed to explore the effect of DKK1 on radiotherapy and immunotherapy in HNSC. We collected the gene expression profile and clinical information of HNSC patients from TCGA, GEO, and ICGC. The immune cell infiltration, level of related pathways and biological processes, signature scores of gene sets of interest were assessed using CIBERSORT, GSEA or GSVA respectively. One of the genes, Dickkopf-1 (DKK1), a secreted protein which plays important roles in the Wnt signaling pathways, was identified because of its significantly higher expression in HNSC. Then, we confirmed the DKK1 expression at protein level by immunohistochemistry of HNSC tissue microarray. CCK8, apoptosis detection and survival curves were performed to investigate the response of DKK1-knockdown HSC-3 cell line to radiation. We found the mRNA and protein expression level of DKK1 was significantly higher in HNSC tissue. The DKK1high group had a shorter survival time in both disease-free survival and overall survival than the DKK1low group. The DKK1high group showed a more immunosuppressive microenvironment with lower infiltration of T cells and higher infiltration of MDSCs. Furthermore, the DKK1high group was enriched in radioresistance related to wound healing, angiogenesis, and autophagy. Patients in the DKK1high group who received radiotherapy had much poorer disease-free survival and overall survival than those in the DKK1low group. HSC-3 cell line was more sensitive to radiation after knockdown of DKK1 by siRNA. Finally, we established a risk score system based on the 9 genes from 41 DKK1-associated immunomodulators and created a nomogram model to predict the prognosis of the patients. Our data show that DKK1 can affect both radiotherapy and immunotherapy in HNSC, suggesting that DKK1 can be a potential target for radioimmunology in HNSC. Citation Format: Xinyu YE, JIAN Zhang, Yi Lu, Yingxuan Gong, Xinyu Jiang, Yueming Li, Yinghao Wang, Xiuzhi Li, Jingwen Liu, Rencui Quan. DKK1 is a potential target for enhancing the efficiency of radioimmunotherapy in head and neck squamous carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5009.
An Active Learning Framework Improves Tumor Variant Interpretation
Authors: Alexandra M. Blee, Bian Li, Turner Pecen, Jens Meiler, Zachary D. Nagel, John A. Capra, Walter J. Chazin
Journal: Cancer Research (2022)

Abstract For precision medicine to reach its full potential for treatment of cancer and other diseases, protein variant effect prediction tools are needed to characterize variants of unknown significance (VUS) in a patient's genome with respect to their likelihood to influence treatment response and outcomes. However, the performance of most variant prediction tools is limited by the difficulty of acquiring sufficient training and validation data. To overcome these limitations, we applied an iterative active learning approach starting from available biochemical, evolutionary, and functional annotations. With active learning, VUS that are most challenging to classify by an initial machine learning model are functionally evaluated and then reincorporated with the phenotype information in subsequent iterations of algorithm training. The potential of active learning to improve variant interpretation was first demonstrated by applying it to synthetic and deep mutational scanning datasets for four cancer-relevant proteins. The utility of the approach to guide interpretation and functional validation of tumor VUS was then probed on the nucleotide excision repair (NER) protein xeroderma pigmentosum complementation group A (XPA), a potential biomarker for cancer therapy sensitivity. A quantitative high-throughput cell-based NER activity assay was used to validate XPA VUS selected by the active learning strategy. In all cases, active learning yielded a significant improvement in variant effect predictions over traditional learning. These analyses suggest that active learning is well suited to significantly improve interpretation of VUS and cancer patient genomes. Significance: A novel machine learning approach predicts the impact of tumor mutations on cellular phenotypes, overcomes limited training data, minimizes costly functional validation, and advances efforts to implement cancer precision medicine.